This is a tricky one and I've always relied on techniques, such as permission-based emails (i.e. only sending to people you have permission to send to) and not using blatantly spamish terminology.
Of late, some of the emails I send out programmatically have started being shuffled into people's spam folder automatically and I'm wondering what I can do about it.
This is despite the fact that these particular emails are not ones that humans would mark as spam, specifically, they are emails that contain license keys that people have paid good money for, so I don't think they're going to consider them spam
I figure this is a big topic in which I am essentially an ignorant simpleton.
Use email authentication methods, such as SPF, and DKIM to prove that your emails and your domain name belong together, and to prevent spoofing of your domain name. The SPF website includes a wizard to generate the DNS information for your site.
Check your reverse DNS to make sure the IP address of your mail server points to the domain name that you use for sending mail.
Make sure that the IP-address that you're using is not on a blacklist
Make sure that the reply-to address is a valid, existing address.
Use the full, real name of the addressee in the To field, not just the email-address (e.g. "John Smith" <john@blacksmiths-international.com> ).
Monitor your abuse accounts, such as abuse@yourdomain.example and postmaster@yourdomain.example. That means - make sure that these accounts exist, read what's sent to them, and act on complaints.
Finally, make it really easy to unsubscribe. Otherwise, your users will unsubscribe by pressing the spam button, and that will affect your reputation.
That said, getting Hotmail to accept your emails remains a black art.